Hi, On 11/07/2012 02:41 PM, Oliver Haddrath wrote: > Hello Sébastian > I had an additional question about the assemblies, what choice is made in the > denovo assembly when >there is allelic variation in the form of indels?
Most assemblers (including Ray) report one of the two alleles because the resulting assembly is haploid. I think that ALLPATHS-LG can report allelic variations in a separate file. > For instance if there are two reads and they vary in length by one or several > base pairs >(representing a real difference between the parental copies) how do you decide >which to include >in the final assembly? Ray uses a deterministic algorithm based on coverage, and branch length. > I assume there is a preset rule and I would be very interested to know what > it is. > many thanks, It is more like a default behavior I guess. > oliver > > -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- > Oliver Haddrath > Dept. of Natural History > Royal Ontario Museum > 100 Queen's Park Cres. > Toronto, Ontario Canada M5S 2C6 > ------------------------------------------------------------------------------ LogMeIn Central: Instant, anywhere, Remote PC access and management. Stay in control, update software, and manage PCs from one command center Diagnose problems and improve visibility into emerging IT issues Automate, monitor and manage. Do more in less time with Central http://p.sf.net/sfu/logmein12331_d2d _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
